Molecular Cell Biology 8th Edition By Harvey Lodish – Test Bank

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5

Fundamental Molecular Genetic Mechanisms

PART A: Linking Concepts and Facts

5.1 Structure of Nucleic Acids

1. In biology the central dogma refers to:

a. protein to DNA to RNA.

b. RNA to DNA to protein.

c. DNA to RNA to protein.

d. RNA to protein to DNA.

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

2. There are four basic molecular processes in a cell, three of which lead to the production of protein. Which of the following shows the correct order?

a. translation, RNA processing, transcription

b. RNA processing, translation, transcription

c. transcription, RNA processing, translation

d. transcription, translation, RNA processing

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

3. Nucleotide bases within a single strand of DNA are held together by which of the following bonds?

a.  phosphodiester 

b. pentose-phosphate 

c. polynucleotide 

d. phosphoester 

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

4. In DNA, which of the following base pairing normally occurs between two strands of DNA?

a.  A to C

b. T to A

c. G to T

d. C to T

Ans: b

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

5. In the laboratory, which of the following two factors are most useful in manipulating DNA?

a. magnesium ions and sugar concentrations

b. UV light and calcium ions

c. formaldehyde and iron ions

d. temperature and pH

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

6. To study the melting temperature (T_m) of your DNA, you have plotted the absorbance of UV light at 260 nm against temperature and have come up with the the following graph. Based on the evidence, the T_m of your double-stranded DNA is approximately:

a. 75 degrees

b. 80 degrees

c. 85 degrees

d. none of the above

Ans: b

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

7. Which of the following is not a constituent of deoxyribonucleotides? 

a. phosphate moieties 

b. deoxyribose 

c. ribose 

d. organic bases 

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

8. Which base pair(s) typically occur(s) in double-stranded DNA? 

a. G·C 

b. G·T 

c. G·A 

d. G·G 

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

9. When the circular double-stranded DNA of certain viruses is underwound, the DNA can twist back on itself and form: 

a. supercoils

b. pseudoknots

c. relaxed coils

d. hairpins

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

10. The ability of DNA to denature is important for which process? 

a. DNA synthesis 

b. nucleic acid hybridization experiments 

c. RNA synthesis 

d. all of the above 

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

5.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA

11. The most common arrangement of protein-coding genes in bacteria are those where the genes encoding proteins that work together are arranged in a contiguous array of DNA called:

a. an operon.

b. a terminator.

c. a promoter.

d. an operator.

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

12. Which of the following are removed from mRNAs during processing? 

a. exons 

b. noncoding sequences 

c. RNA cap structure 

d. poly(A) tail 

Ans: b

Question Type: Multiple Choice

Chapter: 5

Blooms: 

Difficulty: 

13. The base in the wobble position of a codon

a. is the 5´ (first) base. 

b. is the 3´ (third) base.

c. is the second base. 

d. often contains adenine. 

Ans: b

Question Type: Multiple Choice

Chapter: 5

Blooms: 

Difficulty: 

14.  Approximately what percent of all human genes are expressed as alternatively spliced mRNAs?

a. 2

b. 25

c. 50

d. 90

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: 

Difficulty: 

5.3 The Decoding of mRNAs by tRNAs

15. The genetic code is said to be “degenerate” because:

 

a. amino acid sequences are always read in the 3’5’ direction of the mRNA.

b. amino acids are encoded only by DNA sequences found in introns.

c. a particular amino acid can be specified by more than one codon.

d. tryptophan is the first amino acid in all polypeptide chains. 

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

16.  In eukaryotic cells, protein synthesis in the cytoplasm utilizes three types of RNA molecules.  Which of the following contains a three nucleotide sequence called the anticodon?

a. mRNA

b. tRNA

c. rRNA

d. all of the above

Ans. b

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

5.4 Stepwise Synthesis of Proteins on Ribosomes

17. In humans, the ribosome responsible for translating proteins consists of which of following two subunits?

a. 60S and 30S

b. 40S and 50S

c. 18S and 40S

d. 60S and 40S

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

18. Which of the following techniques would you need to use in order to determine the size of the large and small ribosomal subunits in E. coli?

a. X-ray crystallography

b. plaque assay

c. centrifugation

d. hybridization

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Applying, Analyzing

Difficulty: Moderate

19. The first stage of protein translation occurs when Met-tRNA_i^Met base pairs with the mRNA being translated in the ribosomal:

a. P site. 

b. A site.

c. E site.

d. T site.

 

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

20. Which of the following is seen when a single mRNA is simultaneously translated to form multiple copies of a polypeptide chain?

a. phagosome

b. multisome

c. nucleosome

d. polysome

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

21. You are studying polysomes and want to see if their numbers are actually increased in cells translating protein from an expressed retroviral oncogene. Which of the following methods are used to visualize these structures?

a. sedimentation analyses

b. electron microscopy

c. PCR

d. sedimentation analyses and electron microscopy

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Applying, Analyzing

Difficulty: Moderate

22. Which of the following is not a recognized stage of protein synthesis in either prokaryotes or eukaryotes? 

a. elongation 

b. initiation 

c. translation 

d. termination 

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

23. Which of the following factors recognizes the UAG, UAA, and UGA codons? 

a. RNA polymerase 

b. DNA polymerase 

c. termination factors 

d. elongation factors 

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

24. Which codon serves as the start codon in mRNA for translation? 

a. AGU 

b. AUG 

c. UGA 

d. UGG 

Ans: b 

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: : Easy

25. Which of the following is a protein that is involved in translation? 

a. topoisomerase 

b. ribosomal RNA 

c. RNA polymerase 

d. aminoacyl-tRNA synthetase 

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty:  Moderate

26. Which of the following structures interacts with ribosomes? 

a. tRNA 

b. mRNA 

c. rRNA 

d. all of the above 

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

27. Cellular protein synthesis proceeds in which direction? 

a. carboxyl to amino terminus 

b. amino to carboxyl terminus 

c. 3´’ to 5´ 

d. 5´ to 3´ 

Ans: b

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

28. In eukaryotes, the circular structure of mRNA molecules undergoing translation serves to 

a. increase translation efficiency.

b. target the mRNA for destruction.

c. prevent the formation of polysomes.

d. promote the termination step in protein synthesis.

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

29. In which of these polymers are the monomers added one at a time? 

a. DNA 

b. rRNA 

c. protein 

d. all of the above 

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

5.5 DNA Replication

30. Okazaki fragments are small fragments of DNA that eventually are ligated to form which of the following strands of DNA?

a. lagging

b. parent

c. leading

d. joining

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

31. DNA replication begins at sequences called

a. promoters.

b. initiators.

c. origins.

d. Okazaki fragments.

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

32. An enzyme that breaks DNA, dispels the tension, and reseals the strand ahead of a DNA replication growing fork is called a(n) 

a. topoisomerase. 

b. DNA polymerase. 

c. phosphodiesterase. 

d. aminoacyl-tRNA synthetase. 

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

4.6 DNA Repair and Recombination

33. Silent mutations that occur under a variety of conditions in DNA results in which of the following?

a. a stop codon

b. a change of an amino acid to another

c. the formation of an anticodon

d. no change in the amino acid

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

34. Which of the following lead(s) to a point mutation?

a. deamination of a cytosine base into a uracil base

b. benzo(a)pyrene conversion of guanine to a thymine base

c. deamination of 5-methyl cytosine into thymine

d. all of the above

Ans: d

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

35. A Holliday structure is a(n)

a. intermediate in genetic recombination.

b. double-stranded DNA break.

c. collapsed replication fork.

d. thymine-thymine dimer.

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

36. Which of the following are enzymes that play a key role in the base excision repair of nucleotide mismatches and damaged bases?

a.  glycosamines

b. glycosidases

c. glycosylases

d. none of the above

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

37. Thymine–thymine dimers are chemical adducts that develop in the DNA as a result of damage caused by which of the following?

a. UV light

b. X-rays 

c. RNA polymerase reading errors

d. gamma radiation

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

5.7 Viruses: Parasites of the Cellular Genetic System

38. Viruses that use the lytic cycle of growth generally proceed through five general stages. Which one of the following shows the correct order of three of these stages?

a. replication, assembly, adsorption

b. penetration, adsorption, release

c. replication, assembly, release

d. assembly, replication, penetration

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Difficult

39. You have received a saliva sample from a group of veterinarians who think one of the dogs they are treating has rabies. Which of the following techniques would you use to determine not only if this sample contains viral particles, but how many viral particles are in the sample?

a. centrifugation

b. nucleic acid hybridization

c. plaque assay

d. all of the above

Ans: c

Question Type: Multiple Choice

Chapter: 5

Blooms: Applying, Analyzing

Difficulty: Difficult

40. This type of assay can be used to count the number of viral particles in a sample.

a. plaque assay

b. pap smear

c. lytic cycle

d. transformation assay

Ans: a

Question Type: Multiple Choice

Chapter: 5

Blooms: 

Difficulty: 

PART B: Testing on the Concepts

5.1 Structure of Nucleic Acids

41. A double-stranded piece of DNA containing the sequence GCATGGCCACTACCG has a higher Tm than one containing the sequence GAATGGTAACAACTG. Describe the properties of DNA that make this true. 

Ans: The first sequence contains 10/15 G·C base pairs. G·C base pairs are more stable than A·T base pairs because G and C form three hydrogen bonds, whereas A and T form only two. The greater stability conferred by the additional hydrogen bond in G·C base pairs means that this sequence requires more energy (and thus a higher temperature) for denaturation than does the second sequence, which contains 6/15 G·C base pairs. 

Question Type: Essay

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

42. What is the difference between a nucleoside and a nucleotide? 

Ans: Nucleosides contain a base and a sugar without a phosphate.  Nucleotides are nucleosides that have one, two, or three phosphate groups esterified at the 5´ hydroxyl. 

Question Type: Essay

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

43. To incorporate radiolabeled nucleotides into newly synthesized DNA, researchers use -phosphorus32-labeled nucleotides, in a DNA synthesis reaction, where the  denotes the position of the radioactive phosphate moiety.  Explain why the  position and not the  or  position is the best position for the radioactive group in these experiments. 

Ans: When nucleotides are added to the DNA polymer by DNA polymerase, the  phosphate of the incoming nucleotide attaches to the 3´ hydroxyl of the deoxyribose of the preceding residue to form a phosphodiester bond, releasing a pyrophosphate. If the radioactive label were contained on any position other than the  position, then the radioactive group would be present in the released pyrophosphate and not in the DNA chain. 

Question Type: Essay

Chapter: 5

Blooms: Evaluating, Creating

Difficulty: Difficult

5.2 Transcription of Protein-Coding Genes and Formation of Functional mRNA

44. Which parts of the newly synthesized mRNA molecule do not transmit information for the synthesis of protein? 

Ans: The 5´ 7-methylguanylate cap provides stability only and is not used to generate information. Also, the 5´UTR, 3´UTR, and intron sequences in the body of the mRNA molecule do not code for protein sequence either.  The poly(A) tail, which is added to the 3´UTR after mRNA synthesis, is also noncoding. 

Question Type: Essay

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

5.3 The Decoding of mRNAs by tRNAs

45. If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would need 61 different tRNAs.  If there are only 20 amino acids used in protein synthesis, how would you explain this excess number of tRNAs compared to amino acids?  Conversely, how would you explain the fact that some cells contain fewer than 61 tRNAs?

Ans: The number of tRNAs in most cells is more than the 20 amino acids used in protein synthesis because many amino acids have more than one tRNA to which they can attach. The fact that a single tRNA anticodon is able to recognize more than one, but not necessarily every, codon corresponding to an amino acid would explain why some cells have fewer than the expected 61 tRNAs.  This broader recognition occurs because of the nonstandard pairing between bases in the wobble position corresponding to the 3´ base in the mRNA and the complementary 5´ base in the tRNA anticodon. 

Question Type: Essay

Chapter: 5

Blooms: Applying, Analyzing

Difficulty: Moderate

5.4 Stepwise Synthesis of Proteins on Ribosomes

46. When the CAU anticodon of a tRNA^Met was modified to UAC, the anticodon for tRNA^Val, valine aminoacyl-tRNA synthetase recognized the altered tRNA^Met and added valine rather than methionine to it. When the converse modification was made, the altered tRNA^Val containing a CAU anticodon (rather than UAC) was recognized and activated by methionine aminoacyl-tRNA synthetase. What do these data suggest about the mechanism by which aminoacyl-tRNA synthetases recognize their cognate tRNAs? 

Ans: These data suggest that the anticodon region of a tRNA is recognized by the corresponding aminoacyl-tRNA synthetase. However, some tRNAs apparently contain other identity elements that are of primary importance in recognition of these species by the appropriate aminoacyl-tRNA synthetase. 

Question Type: Essay

Chapter: 5

Blooms: Evaluating, Creating

Difficulty: Difficult

47. Many antibiotics, most of which have been isolated from fungi, act by inhibiting initiation, elongation, or termination of peptides during protein synthesis. These compounds have been very useful in the study of protein synthesis, mainly because an individual antibiotic usually interferes with protein synthesis at a single well-defined step in the complex process of translation. Assume that you have isolated a novel antibiotic from the fungus Pilobolus. This antibiotic inhibits bacterial growth and bacterial protein synthesis but does not affect growth or protein synthesis in eukaryotic cells. How could you identify the component of the translational machinery that is affected by this novel antibiotic? 

Ans: Incubation of the radiolabeled antibiotic with cell extracts followed by chromatographic or electrophoretic separation could be used to identify the cell component(s) that binds the antibiotic. In addition, a genetic approach could be taken. The translational components directly involved in the step inhibited by the antibiotic can be identified by growing bacteria in the presence of lethal concentrations of the antibiotic and obtaining mutants that are resistant to its effects. Comparison of the translational components (tRNA, rRNA, initiation and elongation factors, etc.) in the resistant and sensitive cells would likely reveal which component of the translational machinery is altered in the resistant mutant. 

Question Type: Essay

Chapter: 5

Blooms: Evaluating, Creating

Difficulty: Difficult

5.5 DNA Replication

48. The replication of DNA is quite complicated and requires the participation of many different enzymatic activities. These include an RNA polymerase (DNA primase) that synthesizes short segments of RNA, called primers, which are base paired to the DNA template. The 3´-OH ends of these RNA primers serve as initiation sites for the actual DNA polymerase activity. Obviously, DNA primase can synthesize polynucleotides without the benefit of a 3´-OH primer; indeed, it can catalyze the hydrolysis and subsequent linkage of two nucleoside triphosphates without the need for a complementary strand whatsoever. The short segments of RNA must be eliminated and replaced with DNA before replication can be completed. Why do you think that RNA, rather than DNA, primers are employed in the DNA replication process? 

Ans: Because DNA is the molecule of inheritance, replication errors must be scrupulously avoided. Base pairing without a 3´-OH primer, as necessarily performed by any RNA polymerase, is very error prone. If a DNA polymerase performed this function, errors in the DNA sequence (mutations) would be introduced during replication and then transmitted to future generations. An error rate of 1 base in 105, which is not unusual for RNA polymerases, would result in an enormous increase in the mutation rate. However, the RNA primers made during DNA replication are erased and replaced with high-fidelity DNA copies; any mismatched bases will be replaced before being passed on to the next generation.

Question Type: Essay

Chapter: 5

Blooms: Applying, Analyzing

Difficulty: Moderate

5.7 Viruses: Parasites of the Cellular Genetic System

49. What is the difference between lytic and lysogenic bacteriophages? 

Ans: Lytic bacteriophages infect cells, replicate, and lyse the cell as they exit to infect another group of cells. Temperate bacteriophages can either enter the lytic cycle or integrate their genomes into the chromosome of the host bacterium. Once integrated, the phage chromosome replicates as if it were a bacterial gene. With some frequency, the integrated phage chromosome is excised from the bacterial chromosome. At this point, it carries out a lytic cycle to infect additional cells. 

Question Type: Essay

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate

50. Why is the enzyme reverse transcriptase found within retroviral virions? 

Ans: Reverse transcriptase is found within a retrovirus particle because this enzyme is not expressed by the host-cell genome. A retrovirus requires this enzyme to replicate; therefore, it must bring it into the cell along with its genome. 

Question Type: Essay

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Easy

51. Polio virus affects only intestinal cells and motor neurons. By analogy to HIV, explain why only these particular cell types are susceptible to polio infection.

Ans:  Prior to entering the cell, the polio virus binds to specific receptor proteins on the host cell surface. Once the viral particle binds, the virus enters the cell through endocytosis. The only cells that are susceptible to the polio virus are those that have the specific polio virus receptor protein on their surface. 

Question Type: Essay

Chapter: 5

Blooms: Remembering, Understanding

Difficulty: Moderate